Biological Macromolecules Traditional molecular modeling is performed at atomic resolution, which relies on X-ray and NMR experiments to provide structural information. When dealing with biomolecular assemblies of millions of atoms, atomic description of molecular objects becomes very computational inefficient. We developed a method that uses map objects for molecular modeling to efficiently derive structural information from experimental maps, as well as conveniently manipulate map objects, perform conformational search directly using map objects. This development work has been implemented into CHARMM as the EMAP module. This implementation enables CHARMM to manipulate map objects, including map input, output, comparison, docking, etc. Other experiment such as transition metal ion FRET (tmFRET) is becoming a useful way to obtain protein structure information. A new focus of our research is to combine efficient simulation technique with structural information from experiment to assist high throughput protein structure determination. Structure determination from low resolution EM maps We developed a map-restrained self-guided Langevin dynamics (MapSGLD) simulation method for efficient targeted conformational search. The targeted conformational search represents simulations under restraints defined by experimental observations and/or by user specified structural requirements. Through map-restraints, this method provides an efficient way to maintain substructures and to set structure targets during conformational searching. With an enhanced conformational searching ability of self-guided Langevin dynamics, this approach is suitable for simulating large-scale conformational changes, such as the formation of macromolecular assemblies and transitions between different conformational states. A direct application of this method is to determine macromolecular structures by flexible fitting of atomic structures into density maps derived from cryo-electron microscopy. Analysis of waters positions identified by X-ray versus cyro-EM. Correlation between water molecules identified in atomic models of -galactosidase determined by cryo-EM and X-ray crystallography. This work is a collaboration with a cryo-EM laboratory at the National Cancer institute, NIH. It is based on their recently published 2.2- resolution solution structure of -galactosidase, that contains resolved water densities. This study analyses how the water positions determined by cryo-EM compare to conserved water across all crystallography-determined structures. Interactions between water molecules and amino acids occur both at the surface of protein and within the structure, including areas such as subunit interfaces, catalytic sites, and other cavities. Identifying protein solvation profiles are critical to understand both protein structure and function, as well as for the design of high affinity lead compounds for drug discovery. The global organization of protein binding sites. A global organization of protein binding sites is obtained by constructing a weighted network of all known binding sites based on their structural similarities and detecting communities of structurally similar binding sites based on the minimum description length principle. The analysis reveals that there are two central binding site communities that play the roles of the network hubs of smaller peripheral communities. The sizes of communities follow a power-law distribution, which indicates that the binding sites included in larger communities may be older and have been evolutionary structural scaffolds of more recent ones. Structurally similar binding sites in the same community bind to diverse ligands promiscuously and they are also embedded in diverse domain structures. Understanding the general principles of binding site interplay will pave the way for improved drug design and protein design. Structure mechanism of Glutamate receptor activation Ionotropic glutamate receptors are cation channels that mediate signal transmission by depolarizing the postsynapitic membrane in response to L-glutamate release from the presynaptic neuron. Within the iGluR family of receptors are a-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPA), kainite(KA), and N-methyl-D-aspartate (NMDA) subtypes, receptors that are all activated by glutamate and related in amino acid sequence, yet distinct in overall architecture, pharmacology, and biophysical characteristics. AMPA receptors are tetrameric complexes composed of subunits with a modular domain arrangement, beginning with the amino-terminal domain(ATD), the ligand- or agonist-binding domain (LBD), and the pore-forming transmembrane domain (TMD). Because AMPA receptors undergo rapid and nearly complete desensitization in the continued presence of agonist, it has proven difficult to elucidate high-resolution structures of agonist-bound, activated states and to define mechanism by which the chemical potential of agonist binding is transduced into the mechanical force of ion channel gating. The map-restrained self-guided Langevin dynamics (MapSGLD) simulation method we developed previously can utilize structural information embedded in a force field to flexibly fit macromolecular systems into low resolution maps to obtain energetically favored atomic structures that satisfy the maps. We perform flexible fitting with MapSGLD to obtain atomic structures of the glutamate receptor from EM maps. The open state atomic structure of the glutamate receptor shows the LBD in the clamshell closed conformation that agrees with the LBD x-ray structure. In addition to structural determination, MapSGLD provides dynamic information about the transition between different states.